forked from D-Net/dnet-hadoop
bug fix in graph-mapper, changes in the implementation of the openorgs wf to create relations and populate openorgs db
This commit is contained in:
miconis
parent
4b2124a18e
commit
1a85020572
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@ -90,7 +90,10 @@
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-core</artifactId>
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</dependency>
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<dependency>
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<groupId>org.apache.httpcomponents</groupId>
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<artifactId>httpclient</artifactId>
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</dependency>
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</dependencies>
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@ -29,6 +29,7 @@ import eu.dnetlib.pace.config.DedupConfig;
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abstract class AbstractSparkAction implements Serializable {
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protected static final int NUM_PARTITIONS = 1000;
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protected static final int NUM_CONNECTIONS = 20;
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protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
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@ -95,6 +95,11 @@ public class DedupUtility {
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return String.format("%s/%s/%s_simrel", basePath, actionSetId, entityType);
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}
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public static String createOpenorgsMergeRelsPath(
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final String basePath, final String actionSetId, final String entityType) {
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return String.format("%s/%s/%s_openorgs_mergerels", basePath, actionSetId, entityType);
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}
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public static String createMergeRelPath(
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final String basePath, final String actionSetId, final String entityType) {
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return String.format("%s/%s/%s_mergerel", basePath, actionSetId, entityType);
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@ -6,6 +6,7 @@ import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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@ -19,6 +20,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -34,7 +36,7 @@ public class SparkCopyOpenorgs extends AbstractSparkAction {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateSimRels.class
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SparkCopyOpenorgs.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgs_parameters.json")));
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parser.parseArgument(args);
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@ -72,7 +74,7 @@ public class SparkCopyOpenorgs extends AbstractSparkAction {
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final Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
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filterEntities(spark, entityPath, clazz)
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filterOpenorgs(spark, entityPath)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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@ -80,21 +82,20 @@ public class SparkCopyOpenorgs extends AbstractSparkAction {
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}
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public static <T extends OafEntity> Dataset<T> filterEntities(
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public static Dataset<Organization> filterOpenorgs(
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final SparkSession spark,
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final String entitiesInputPath,
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final Class<T> clazz) {
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final String entitiesInputPath) {
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// <id, json_entity>
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Dataset<T> entities = spark
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.read()
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.textFile(entitiesInputPath)
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.map(
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(MapFunction<String, T>) it -> {
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T entity = OBJECT_MAPPER.readValue(it, clazz);
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return entity;
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},
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Encoders.kryo(clazz));
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Dataset<Organization> entities = spark
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.createDataset(
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sc
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.textFile(entitiesInputPath)
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.map(it -> OBJECT_MAPPER.readValue(it, Organization.class))
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.rdd(),
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Encoders.bean(Organization.class));
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entities.show();
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return entities.filter(entities.col("id").contains("openorgs____"));
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}
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@ -6,14 +6,13 @@ import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.pace.config.DedupConfig;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.dom4j.DocumentException;
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import org.slf4j.Logger;
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@ -21,10 +20,13 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.config.DedupConfig;
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//copy simrels (verified) from relation to the workdir in order to make them available for the deduplication
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public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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@ -83,17 +85,17 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(this::isOpenorgs) //takes only relations coming from openorgs
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.filter(this::filterOpenorgsRels) //takes only isSimilarTo relations between organizations from openorgs
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.filter(this::excludeOpenorgsMesh) //excludes relations between an organization and an openorgsmesh
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.filter(this::excludeNonOpenorgs); //excludes relations with no openorgs id involved
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.filter(this::isOpenorgs) // takes only relations coming from openorgs
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.filter(this::filterOpenorgsRels) // takes only isSimilarTo relations between organizations from openorgs
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.filter(this::excludeOpenorgsMesh) // excludes relations between an organization and an openorgsmesh
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.filter(this::excludeNonOpenorgs); // excludes relations with no openorgs id involved
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//turn openorgs isSimilarTo relations into mergerels
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JavaRDD<Relation> mergeRels = rawRels.flatMap(rel -> {
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// turn openorgs isSimilarTo relations into mergerels
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JavaRDD<Relation> mergeRelsRDD = rawRels.flatMap(rel -> {
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List<Relation> mergerels = new ArrayList<>();
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String openorgsId = rel.getSource().contains("openorgs____")? rel.getSource() : rel.getTarget();
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String mergedId = rel.getSource().contains("openorgs____")? rel.getTarget() : rel.getSource();
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String openorgsId = rel.getSource().contains("openorgs____") ? rel.getSource() : rel.getTarget();
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String mergedId = rel.getSource().contains("openorgs____") ? rel.getTarget() : rel.getSource();
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mergerels.add(rel(openorgsId, mergedId, "merges", dedupConf));
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mergerels.add(rel(mergedId, openorgsId, "isMergedIn", dedupConf));
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@ -101,7 +103,13 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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return mergerels.iterator();
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});
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mergeRels.saveAsTextFile(outputPath);
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spark
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.createDataset(
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mergeRelsRDD.rdd(),
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Encoders.bean(Relation.class))
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.write()
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.mode(SaveMode.Append)
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.parquet(outputPath);
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}
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private static MapFunction<String, Relation> patchRelFn() {
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@ -116,7 +124,8 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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private boolean filterOpenorgsRels(Relation rel) {
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization") && rel.getSubRelType().equals("dedup"))
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization")
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&& rel.getSubRelType().equals("dedup"))
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return true;
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return false;
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}
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@ -124,7 +133,7 @@ public class SparkCopyOpenorgsMergeRels extends AbstractSparkAction {
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private boolean isOpenorgs(Relation rel) {
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k: rel.getCollectedfrom()) {
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for (KeyValue k : rel.getCollectedfrom()) {
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if (k.getValue().equals("OpenOrgs Database")) {
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return true;
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}
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@ -6,13 +6,13 @@ import java.util.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.pace.config.DedupConfig;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.graphx.Edge;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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@ -22,97 +22,98 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.config.DedupConfig;
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//copy simrels (verified) from relation to the workdir in order to make them available for the deduplication
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public class SparkCopyOpenorgsSimRels extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCopyOpenorgsMergeRels.class);
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private static final Logger log = LoggerFactory.getLogger(SparkCopyOpenorgsSimRels.class);
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public SparkCopyOpenorgsSimRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public SparkCopyOpenorgsSimRels(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgsSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
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parser.parseArgument(args);
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCopyOpenorgsSimRels.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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new SparkCopyOpenorgsSimRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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SparkConf conf = new SparkConf();
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new SparkCopyOpenorgsSimRels(parser, getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
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}
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@Override
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public void run(ISLookUpService isLookUpService)
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throws DocumentException, IOException, ISLookUpException {
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@Override
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public void run(ISLookUpService isLookUpService)
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throws DocumentException, IOException, ISLookUpException {
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// read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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// read oozie parameters
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final String graphBasePath = parser.get("graphBasePath");
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final String actionSetId = parser.get("actionSetId");
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final String workingPath = parser.get("workingPath");
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final int numPartitions = Optional
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.ofNullable(parser.get("numPartitions"))
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.map(Integer::valueOf)
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.orElse(NUM_PARTITIONS);
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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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log.info("numPartitions: '{}'", numPartitions);
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log.info("graphBasePath: '{}'", graphBasePath);
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log.info("actionSetId: '{}'", actionSetId);
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log.info("workingPath: '{}'", workingPath);
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log.info("Copying OpenOrgs SimRels");
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log.info("Copying OpenOrgs SimRels");
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final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, "organization");
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final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, "organization");
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removeOutputDir(spark, outputPath);
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
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Dataset<Relation> rawRels = spark
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.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.filter(this::filterOpenorgsRels);
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JavaRDD<Relation> rawRels = spark
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.read()
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.textFile(relationPath)
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.map(patchRelFn(), Encoders.bean(Relation.class))
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.toJavaRDD()
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.filter(this::isOpenorgs)
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.filter(this::filterOpenorgsRels);
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save(rawRels, outputPath, SaveMode.Append);
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save(spark.createDataset(rawRels.rdd(),Encoders.bean(Relation.class)), outputPath, SaveMode.Append);
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}
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log.info("Copied " + rawRels.count() + " Similarity Relations");
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private static MapFunction<String, Relation> patchRelFn() {
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return value -> {
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final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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return rel;
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};
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}
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private boolean filterOpenorgsRels(Relation rel) {
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private boolean filterOpenorgsRels(Relation rel) {
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization") && rel.getSubRelType().equals("dedup"))
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return true;
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return false;
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}
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if (rel.getRelClass().equals("isSimilarTo") && rel.getRelType().equals("organizationOrganization")
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&& rel.getSubRelType().equals("dedup") && isOpenorgs(rel))
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return true;
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return false;
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}
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private boolean isOpenorgs(Relation rel) {
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private boolean isOpenorgs(Relation rel) {
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k: rel.getCollectedfrom()) {
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if (k.getValue().equals("OpenOrgs Database")) {
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return true;
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}
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}
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}
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return false;
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}
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if (rel.getCollectedfrom() != null) {
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for (KeyValue k : rel.getCollectedfrom()) {
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if (k.getValue() != null && k.getValue().equals("OpenOrgs Database")) {
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return true;
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}
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}
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}
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return false;
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}
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}
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@ -1,12 +1,9 @@
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package eu.dnetlib.dhp.oa.dedup;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import java.io.IOException;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileStatus;
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@ -19,92 +16,95 @@ import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.dom4j.DocumentException;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import scala.Tuple2;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Optional;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class);
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class);
|
||||
|
||||
private static final String IDJSONPATH = "$.id";
|
||||
public SparkCopyRelationsNoOpenorgs(ArgumentApplicationParser parser, SparkSession spark) {
|
||||
super(parser, spark);
|
||||
}
|
||||
|
||||
public SparkCopyRelationsNoOpenorgs(ArgumentApplicationParser parser, SparkSession spark) {
|
||||
super(parser, spark);
|
||||
}
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyRelationsNoOpenorgs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyRelationsNoOpenorgs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
new SparkUpdateEntity(parser, getSparkSession(conf))
|
||||
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
|
||||
new SparkUpdateEntity(parser, getSparkSession(conf))
|
||||
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
public void run(ISLookUpService isLookUpService) throws IOException {
|
||||
|
||||
public void run(ISLookUpService isLookUpService) throws IOException {
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final String dedupGraphPath = parser.get("dedupGraphPath");
|
||||
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final String dedupGraphPath = parser.get("dedupGraphPath");
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("dedupGraphPath: '{}'", dedupGraphPath);
|
||||
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("dedupGraphPath: '{}'", dedupGraphPath);
|
||||
final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
|
||||
final String outputPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
removeOutputDir(spark, outputPath);
|
||||
|
||||
final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
|
||||
final String outputPath = DedupUtility.createEntityPath(dedupGraphPath, "relation");
|
||||
JavaRDD<Relation> simRels = spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(patchRelFn(), Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(this::excludeOpenorgsRels);
|
||||
|
||||
removeOutputDir(spark, outputPath);
|
||||
spark
|
||||
.createDataset(simRels.rdd(), Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(outputPath);
|
||||
|
||||
JavaRDD<Relation> simRels = spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(patchRelFn(), Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(this::excludeOpenorgsRels);
|
||||
}
|
||||
|
||||
simRels.saveAsTextFile(outputPath);
|
||||
private static MapFunction<String, Relation> patchRelFn() {
|
||||
return value -> {
|
||||
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
|
||||
if (rel.getDataInfo() == null) {
|
||||
rel.setDataInfo(new DataInfo());
|
||||
}
|
||||
return rel;
|
||||
};
|
||||
}
|
||||
|
||||
}
|
||||
private boolean excludeOpenorgsRels(Relation rel) {
|
||||
|
||||
private static MapFunction<String, Relation> patchRelFn() {
|
||||
return value -> {
|
||||
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
|
||||
if (rel.getDataInfo() == null) {
|
||||
rel.setDataInfo(new DataInfo());
|
||||
}
|
||||
return rel;
|
||||
};
|
||||
}
|
||||
|
||||
private boolean excludeOpenorgsRels(Relation rel) {
|
||||
|
||||
if (rel.getCollectedfrom() != null) {
|
||||
for (KeyValue k: rel.getCollectedfrom()) {
|
||||
if (k.getValue().equals("OpenOrgs Database")) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
}
|
||||
return true;
|
||||
}
|
||||
if (rel.getCollectedfrom() != null) {
|
||||
for (KeyValue k : rel.getCollectedfrom()) {
|
||||
if (k.getValue().equals("OpenOrgs Database")) {
|
||||
return false;
|
||||
}
|
||||
}
|
||||
}
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -10,6 +10,7 @@ import org.apache.spark.api.java.JavaPairRDD;
|
|||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.PairFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
|
|
@ -81,7 +82,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
|
|||
log.info("Creating simrels for: '{}'", subEntity);
|
||||
|
||||
final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
|
||||
removeOutputDir(spark, outputPath);
|
||||
|
||||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
|
|
@ -99,13 +99,19 @@ public class SparkCreateSimRels extends AbstractSparkAction {
|
|||
.createSortedBlocks(mapDocuments, dedupConf)
|
||||
.repartition(numPartitions);
|
||||
|
||||
// create relations by comparing only elements in the same group
|
||||
Deduper
|
||||
.computeRelations(sc, blocks, dedupConf)
|
||||
.map(t -> createSimRel(t._1(), t._2(), entity))
|
||||
.repartition(numPartitions)
|
||||
.map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath);
|
||||
Dataset<Relation> simRels = spark
|
||||
.createDataset(
|
||||
Deduper
|
||||
.computeRelations(sc, blocks, dedupConf)
|
||||
.map(t -> createSimRel(t._1(), t._2(), entity))
|
||||
.repartition(numPartitions)
|
||||
.rdd(),
|
||||
Encoders.bean(Relation.class));
|
||||
|
||||
save(simRels, outputPath, SaveMode.Append);
|
||||
|
||||
log.info("Generated " + simRels.count() + " Similarity Relations");
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,249 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Optional;
|
||||
import java.util.Properties;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.dedup.model.OrgSimRel;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class SparkPrepareNewOrgs extends AbstractSparkAction {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkPrepareNewOrgs.class);
|
||||
|
||||
public SparkPrepareNewOrgs(ArgumentApplicationParser parser, SparkSession spark) {
|
||||
super(parser, spark);
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkPrepareNewOrgs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/prepareNewOrgs_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
|
||||
new SparkPrepareNewOrgs(parser, getSparkSession(conf))
|
||||
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run(ISLookUpService isLookUpService) throws IOException {
|
||||
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
final String actionSetId = parser.get("actionSetId");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final int numConnections = Optional
|
||||
.ofNullable(parser.get("numConnections"))
|
||||
.map(Integer::valueOf)
|
||||
.orElse(NUM_CONNECTIONS);
|
||||
|
||||
final String apiUrl = Optional
|
||||
.ofNullable(parser.get("apiUrl"))
|
||||
.orElse("");
|
||||
|
||||
final String dbUrl = parser.get("dbUrl");
|
||||
final String dbTable = parser.get("dbTable");
|
||||
final String dbUser = parser.get("dbUser");
|
||||
final String dbPwd = parser.get("dbPwd");
|
||||
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("isLookUpUrl: '{}'", isLookUpUrl);
|
||||
log.info("actionSetId: '{}'", actionSetId);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("numPartitions: '{}'", numConnections);
|
||||
log.info("apiUrl: '{}'", apiUrl);
|
||||
log.info("dbUrl: '{}'", dbUrl);
|
||||
log.info("dbUser: '{}'", dbUser);
|
||||
log.info("table: '{}'", dbTable);
|
||||
log.info("dbPwd: '{}'", "xxx");
|
||||
|
||||
final String entityPath = DedupUtility.createEntityPath(graphBasePath, "organization");
|
||||
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
|
||||
final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
|
||||
|
||||
Dataset<OrgSimRel> newOrgs = createNewOrgs(spark, mergeRelPath, relationPath, entityPath);
|
||||
|
||||
final Properties connectionProperties = new Properties();
|
||||
connectionProperties.put("user", dbUser);
|
||||
connectionProperties.put("password", dbPwd);
|
||||
|
||||
log.info("Number of New Organization created: '{}'", newOrgs.count());
|
||||
|
||||
newOrgs
|
||||
.repartition(numConnections)
|
||||
.write()
|
||||
.mode(SaveMode.Append)
|
||||
.jdbc(dbUrl, dbTable, connectionProperties);
|
||||
|
||||
if (!apiUrl.isEmpty())
|
||||
updateSimRels(apiUrl);
|
||||
|
||||
}
|
||||
|
||||
public static Dataset<OrgSimRel> createNewOrgs(
|
||||
final SparkSession spark,
|
||||
final String mergeRelsPath,
|
||||
final String relationPath,
|
||||
final String entitiesPath) {
|
||||
|
||||
// collect diffrels from the raw graph relations: <other id, "diffRel">
|
||||
JavaPairRDD<String, String> diffRels = spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(patchRelFn(), Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(r -> filterRels(r, "organization"))
|
||||
// take the worst id of the diffrel: <other id, "diffRel">
|
||||
.mapToPair(rel -> {
|
||||
if (compareIds(rel.getSource(), rel.getTarget()) > 0)
|
||||
return new Tuple2<>(rel.getSource(), "diffRel");
|
||||
else
|
||||
return new Tuple2<>(rel.getTarget(), "diffRel");
|
||||
})
|
||||
.distinct();
|
||||
log.info("Number of DiffRels collected: '{}'", diffRels.count());
|
||||
|
||||
// collect entities: <id, json_entity>
|
||||
Dataset<Tuple2<String, Organization>> entities = spark
|
||||
.read()
|
||||
.textFile(entitiesPath)
|
||||
.map(
|
||||
(MapFunction<String, Tuple2<String, Organization>>) it -> {
|
||||
Organization entity = OBJECT_MAPPER.readValue(it, Organization.class);
|
||||
return new Tuple2<>(entity.getId(), entity);
|
||||
},
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Organization.class)));
|
||||
|
||||
// collect mergerels and remove ids in the diffrels
|
||||
Dataset<Tuple2<String, String>> openorgsRels = spark
|
||||
.createDataset(
|
||||
spark
|
||||
.read()
|
||||
.load(mergeRelsPath)
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.where("relClass == 'isMergedIn'")
|
||||
.toJavaRDD()
|
||||
.mapToPair(r -> new Tuple2<>(r.getSource(), r.getTarget())) // <id, dedup_id>
|
||||
.leftOuterJoin(diffRels) // <target, "diffRel">
|
||||
.filter(rel -> !rel._2()._2().isPresent())
|
||||
.mapToPair(rel -> new Tuple2<>(rel._1(), rel._2()._1()))
|
||||
.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
log.info("Number of Openorgs Relations loaded: '{}'", openorgsRels.count());
|
||||
|
||||
return entities
|
||||
.joinWith(openorgsRels, entities.col("_1").equalTo(openorgsRels.col("_1")), "left")
|
||||
.filter((FilterFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>>) t -> t._2() == null)
|
||||
// take entities not in mergerels (they are single entities, therefore are new orgs)
|
||||
.filter(
|
||||
(FilterFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>>) t -> !t
|
||||
._1()
|
||||
._1()
|
||||
.contains("openorgs"))
|
||||
// exclude openorgs, don't need to propose them as new orgs
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, Organization>, Tuple2<String, String>>, OrgSimRel>) r -> new OrgSimRel(
|
||||
"",
|
||||
r._1()._2().getOriginalId().get(0),
|
||||
r._1()._2().getLegalname() != null ? r._1()._2().getLegalname().getValue() : "",
|
||||
r._1()._2().getLegalshortname() != null ? r._1()._2().getLegalshortname().getValue() : "",
|
||||
r._1()._2().getCountry() != null ? r._1()._2().getCountry().getClassid() : "",
|
||||
r._1()._2().getWebsiteurl() != null ? r._1()._2().getWebsiteurl().getValue() : "",
|
||||
r._1()._2().getCollectedfrom().get(0).getValue(), ""),
|
||||
Encoders.bean(OrgSimRel.class));
|
||||
|
||||
}
|
||||
|
||||
private static String updateSimRels(final String apiUrl) throws IOException {
|
||||
|
||||
log.info("Updating simrels on the portal");
|
||||
|
||||
final HttpGet req = new HttpGet(apiUrl);
|
||||
try (final CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
try (final CloseableHttpResponse response = client.execute(req)) {
|
||||
return IOUtils.toString(response.getEntity().getContent());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
private static MapFunction<String, Relation> patchRelFn() {
|
||||
return value -> {
|
||||
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
|
||||
if (rel.getDataInfo() == null) {
|
||||
rel.setDataInfo(new DataInfo());
|
||||
}
|
||||
return rel;
|
||||
};
|
||||
}
|
||||
|
||||
public static int compareIds(String o1, String o2) {
|
||||
if (o1.contains("openorgs____") && o2.contains("openorgs____"))
|
||||
return o1.compareTo(o2);
|
||||
if (o1.contains("corda") && o2.contains("corda"))
|
||||
return o1.compareTo(o2);
|
||||
|
||||
if (o1.contains("openorgs____"))
|
||||
return -1;
|
||||
if (o2.contains("openorgs____"))
|
||||
return 1;
|
||||
|
||||
if (o1.contains("corda"))
|
||||
return -1;
|
||||
if (o2.contains("corda"))
|
||||
return 1;
|
||||
|
||||
return o1.compareTo(o2);
|
||||
}
|
||||
|
||||
private static boolean filterRels(Relation rel, String entityType) {
|
||||
|
||||
switch (entityType) {
|
||||
case "result":
|
||||
if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("resultResult")
|
||||
&& rel.getSubRelType().equals("dedup"))
|
||||
return true;
|
||||
break;
|
||||
case "organization":
|
||||
if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("organizationOrganization")
|
||||
&& rel.getSubRelType().equals("dedup"))
|
||||
return true;
|
||||
break;
|
||||
default:
|
||||
return false;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,341 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
import java.util.stream.StreamSupport;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SaveMode;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.google.common.collect.Lists;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.dedup.model.OrgSimRel;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import scala.Tuple2;
|
||||
import scala.Tuple3;
|
||||
|
||||
public class SparkPrepareOrgRels extends AbstractSparkAction {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkPrepareOrgRels.class);
|
||||
|
||||
public SparkPrepareOrgRels(ArgumentApplicationParser parser, SparkSession spark) {
|
||||
super(parser, spark);
|
||||
}
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/prepareOrgRels_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
||||
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
||||
|
||||
new SparkPrepareOrgRels(parser, getSparkSession(conf))
|
||||
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run(ISLookUpService isLookUpService) throws IOException {
|
||||
|
||||
final String graphBasePath = parser.get("graphBasePath");
|
||||
final String isLookUpUrl = parser.get("isLookUpUrl");
|
||||
final String actionSetId = parser.get("actionSetId");
|
||||
final String workingPath = parser.get("workingPath");
|
||||
final int numConnections = Optional
|
||||
.ofNullable(parser.get("numConnections"))
|
||||
.map(Integer::valueOf)
|
||||
.orElse(NUM_CONNECTIONS);
|
||||
|
||||
final String dbUrl = parser.get("dbUrl");
|
||||
final String dbTable = parser.get("dbTable");
|
||||
final String dbUser = parser.get("dbUser");
|
||||
final String dbPwd = parser.get("dbPwd");
|
||||
|
||||
log.info("graphBasePath: '{}'", graphBasePath);
|
||||
log.info("isLookUpUrl: '{}'", isLookUpUrl);
|
||||
log.info("actionSetId: '{}'", actionSetId);
|
||||
log.info("workingPath: '{}'", workingPath);
|
||||
log.info("numPartitions: '{}'", numConnections);
|
||||
log.info("dbUrl: '{}'", dbUrl);
|
||||
log.info("dbUser: '{}'", dbUser);
|
||||
log.info("table: '{}'", dbTable);
|
||||
log.info("dbPwd: '{}'", "xxx");
|
||||
|
||||
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, actionSetId, "organization");
|
||||
final String entityPath = DedupUtility.createEntityPath(graphBasePath, "organization");
|
||||
final String relationPath = DedupUtility.createEntityPath(graphBasePath, "relation");
|
||||
|
||||
Dataset<OrgSimRel> relations = createRelations(spark, mergeRelPath, relationPath, entityPath);
|
||||
|
||||
final Properties connectionProperties = new Properties();
|
||||
connectionProperties.put("user", dbUser);
|
||||
connectionProperties.put("password", dbPwd);
|
||||
|
||||
relations
|
||||
.repartition(numConnections)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.jdbc(dbUrl, dbTable, connectionProperties);
|
||||
|
||||
}
|
||||
|
||||
private static boolean filterRels(Relation rel, String entityType) {
|
||||
|
||||
switch (entityType) {
|
||||
case "result":
|
||||
if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("resultResult")
|
||||
&& rel.getSubRelType().equals("dedup"))
|
||||
return true;
|
||||
break;
|
||||
case "organization":
|
||||
if (rel.getRelClass().equals("isDifferentFrom") && rel.getRelType().equals("organizationOrganization")
|
||||
&& rel.getSubRelType().equals("dedup"))
|
||||
return true;
|
||||
break;
|
||||
default:
|
||||
return false;
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
// create openorgs simrels <best id, other id> starting from mergerels, remove the diffrels
|
||||
public static Dataset<OrgSimRel> createRelations(
|
||||
final SparkSession spark,
|
||||
final String mergeRelsPath,
|
||||
final String relationPath,
|
||||
final String entitiesPath) {
|
||||
|
||||
// collect diffrels from the raw graph relations: <<best id, other id>, "diffRel">
|
||||
JavaRDD<Tuple2<Tuple2<String, String>, String>> diffRels = spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(patchRelFn(), Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(r -> filterRels(r, "organization"))
|
||||
// put the best id as source of the diffrel: <best id, other id>
|
||||
.map(rel -> {
|
||||
if (compareIds(rel.getSource(), rel.getTarget()) < 0)
|
||||
return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "diffRel");
|
||||
else
|
||||
return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "diffRel");
|
||||
})
|
||||
.distinct();
|
||||
log.info("Number of DiffRels collected: {}", diffRels.count());
|
||||
|
||||
// collect all the organizations
|
||||
Dataset<Tuple2<String, Organization>> entities = spark
|
||||
.read()
|
||||
.textFile(entitiesPath)
|
||||
.map(
|
||||
(MapFunction<String, Tuple2<String, Organization>>) it -> {
|
||||
Organization entity = OBJECT_MAPPER.readValue(it, Organization.class);
|
||||
return new Tuple2<>(entity.getId(), entity);
|
||||
},
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Organization.class)));
|
||||
|
||||
// relations with their group (connected component id)
|
||||
JavaRDD<Tuple2<Tuple2<String, String>, String>> rawOpenorgsRels = spark
|
||||
.read()
|
||||
.load(mergeRelsPath)
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.where("relClass == 'merges'")
|
||||
.toJavaRDD()
|
||||
.mapToPair(r -> new Tuple2<>(r.getSource(), r.getTarget()))
|
||||
.filter(t -> !t._2().contains("openorgsmesh")) // remove openorgsmesh: they are only for dedup
|
||||
.groupByKey()
|
||||
.map(g -> Lists.newArrayList(g._2()))
|
||||
.filter(l -> l.size() > 1)
|
||||
.flatMap(l -> {
|
||||
String groupId = "group::" + UUID.randomUUID();
|
||||
List<String> ids = sortIds(l); // sort IDs by type
|
||||
List<Tuple2<Tuple2<String, String>, String>> rels = new ArrayList<>();
|
||||
String source = ids.get(0);
|
||||
for (String target : ids) {
|
||||
rels.add(new Tuple2<>(new Tuple2<>(source, target), groupId));
|
||||
}
|
||||
|
||||
return rels.iterator();
|
||||
});
|
||||
log.info("Number of Raw Openorgs Relations created: {}", rawOpenorgsRels.count());
|
||||
|
||||
// filter out diffRels
|
||||
JavaRDD<Tuple3<String, String, String>> openorgsRels = rawOpenorgsRels
|
||||
.union(diffRels)
|
||||
// concatenation of source and target: <source|||target, group id> or <source|||target, "diffRel">
|
||||
.mapToPair(t -> new Tuple2<>(t._1()._1() + "@@@" + t._1()._2(), t._2()))
|
||||
.groupByKey()
|
||||
.map(
|
||||
g -> new Tuple2<>(g._1(), StreamSupport
|
||||
.stream(g._2().spliterator(), false)
|
||||
.collect(Collectors.toList())))
|
||||
// <source|||target, list(group_id, "diffRel")>: take only relations with only the group_id, it
|
||||
// means they are correct. If the diffRel is present the relation has to be removed
|
||||
.filter(g -> g._2().size() == 1 && g._2().get(0).contains("group::"))
|
||||
.map(
|
||||
t -> new Tuple3<>(
|
||||
t._1().split("@@@")[0],
|
||||
t._1().split("@@@")[1],
|
||||
t._2().get(0)));
|
||||
log.info("Number of Openorgs Relations created: '{}'", openorgsRels.count());
|
||||
|
||||
// <best ID basing on priority, ID, groupID>
|
||||
Dataset<Tuple3<String, String, String>> relations = spark
|
||||
.createDataset(
|
||||
openorgsRels.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
// create orgsimrels
|
||||
Dataset<Tuple2<String, OrgSimRel>> relations2 = relations
|
||||
.joinWith(entities, relations.col("_2").equalTo(entities.col("_1")), "inner")
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple3<String, String, String>, Tuple2<String, Organization>>, OrgSimRel>) r -> new OrgSimRel(
|
||||
r._1()._1(),
|
||||
r._2()._2().getOriginalId().get(0),
|
||||
r._2()._2().getLegalname() != null ? r._2()._2().getLegalname().getValue() : "",
|
||||
r._2()._2().getLegalshortname() != null ? r._2()._2().getLegalshortname().getValue() : "",
|
||||
r._2()._2().getCountry() != null ? r._2()._2().getCountry().getClassid() : "",
|
||||
r._2()._2().getWebsiteurl() != null ? r._2()._2().getWebsiteurl().getValue() : "",
|
||||
r._2()._2().getCollectedfrom().get(0).getValue(),
|
||||
r._1()._3()),
|
||||
Encoders.bean(OrgSimRel.class))
|
||||
.map(
|
||||
(MapFunction<OrgSimRel, Tuple2<String, OrgSimRel>>) o -> new Tuple2<>(o.getLocal_id(), o),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.bean(OrgSimRel.class)));
|
||||
|
||||
return relations2
|
||||
.joinWith(entities, relations2.col("_1").equalTo(entities.col("_1")), "inner")
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, OrgSimRel>, Tuple2<String, Organization>>, OrgSimRel>) r -> {
|
||||
OrgSimRel orgSimRel = r._1()._2();
|
||||
orgSimRel.setLocal_id(r._2()._2().getOriginalId().get(0));
|
||||
return orgSimRel;
|
||||
},
|
||||
Encoders.bean(OrgSimRel.class));
|
||||
|
||||
}
|
||||
|
||||
public static int compareIds(String o1, String o2) {
|
||||
if (o1.contains("openorgs____") && o2.contains("openorgs____"))
|
||||
return o1.compareTo(o2);
|
||||
if (o1.contains("corda") && o2.contains("corda"))
|
||||
return o1.compareTo(o2);
|
||||
|
||||
if (o1.contains("openorgs____"))
|
||||
return -1;
|
||||
if (o2.contains("openorgs____"))
|
||||
return 1;
|
||||
|
||||
if (o1.contains("corda"))
|
||||
return -1;
|
||||
if (o2.contains("corda"))
|
||||
return 1;
|
||||
|
||||
return o1.compareTo(o2);
|
||||
}
|
||||
|
||||
// Sort IDs basing on the type. Priority: 1) openorgs, 2)corda, 3)alphabetic
|
||||
public static List<String> sortIds(List<String> ids) {
|
||||
ids.sort((o1, o2) -> compareIds(o1, o2));
|
||||
return ids;
|
||||
}
|
||||
|
||||
public static Dataset<OrgSimRel> createRelationsFromScratch(
|
||||
final SparkSession spark,
|
||||
final String mergeRelsPath,
|
||||
final String entitiesPath) {
|
||||
|
||||
// <id, json_entity>
|
||||
Dataset<Tuple2<String, Organization>> entities = spark
|
||||
.read()
|
||||
.textFile(entitiesPath)
|
||||
.map(
|
||||
(MapFunction<String, Tuple2<String, Organization>>) it -> {
|
||||
Organization entity = OBJECT_MAPPER.readValue(it, Organization.class);
|
||||
return new Tuple2<>(entity.getId(), entity);
|
||||
},
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.kryo(Organization.class)));
|
||||
|
||||
Dataset<Tuple2<String, String>> relations = spark
|
||||
.createDataset(
|
||||
spark
|
||||
.read()
|
||||
.load(mergeRelsPath)
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.where("relClass == 'merges'")
|
||||
.toJavaRDD()
|
||||
.mapToPair(r -> new Tuple2<>(r.getSource(), r.getTarget()))
|
||||
.groupByKey()
|
||||
.flatMap(g -> {
|
||||
List<Tuple2<String, String>> rels = new ArrayList<>();
|
||||
for (String id1 : g._2()) {
|
||||
for (String id2 : g._2()) {
|
||||
if (!id1.equals(id2))
|
||||
if (id1.contains("openorgs____") && !id2.contains("openorgsmesh"))
|
||||
rels.add(new Tuple2<>(id1, id2));
|
||||
}
|
||||
}
|
||||
return rels.iterator();
|
||||
})
|
||||
.rdd(),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
Dataset<Tuple2<String, OrgSimRel>> relations2 = relations // <openorgs, corda>
|
||||
.joinWith(entities, relations.col("_2").equalTo(entities.col("_1")), "inner")
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, Organization>>, OrgSimRel>) r -> new OrgSimRel(
|
||||
r._1()._1(),
|
||||
r._2()._2().getOriginalId().get(0),
|
||||
r._2()._2().getLegalname() != null ? r._2()._2().getLegalname().getValue() : "",
|
||||
r._2()._2().getLegalshortname() != null ? r._2()._2().getLegalshortname().getValue() : "",
|
||||
r._2()._2().getCountry() != null ? r._2()._2().getCountry().getClassid() : "",
|
||||
r._2()._2().getWebsiteurl() != null ? r._2()._2().getWebsiteurl().getValue() : "",
|
||||
r._2()._2().getCollectedfrom().get(0).getValue(),
|
||||
"group::" + r._1()._1()),
|
||||
Encoders.bean(OrgSimRel.class))
|
||||
.map(
|
||||
(MapFunction<OrgSimRel, Tuple2<String, OrgSimRel>>) o -> new Tuple2<>(o.getLocal_id(), o),
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.bean(OrgSimRel.class)));
|
||||
|
||||
return relations2
|
||||
.joinWith(entities, relations2.col("_1").equalTo(entities.col("_1")), "inner")
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, OrgSimRel>, Tuple2<String, Organization>>, OrgSimRel>) r -> {
|
||||
OrgSimRel orgSimRel = r._1()._2();
|
||||
orgSimRel.setLocal_id(r._2()._2().getOriginalId().get(0));
|
||||
return orgSimRel;
|
||||
},
|
||||
Encoders.bean(OrgSimRel.class));
|
||||
|
||||
}
|
||||
|
||||
private static MapFunction<String, Relation> patchRelFn() {
|
||||
return value -> {
|
||||
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
|
||||
if (rel.getDataInfo() == null) {
|
||||
rel.setDataInfo(new DataInfo());
|
||||
}
|
||||
return rel;
|
||||
};
|
||||
}
|
||||
}
|
||||
|
|
@ -27,6 +27,8 @@ import org.dom4j.DocumentException;
|
|||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.google.common.collect.Iterables;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.dedup.graph.ConnectedComponent;
|
||||
import eu.dnetlib.dhp.oa.dedup.graph.GraphProcessor;
|
||||
|
|
@ -95,6 +97,9 @@ public class SparkRemoveDiffRels extends AbstractSparkAction {
|
|||
|
||||
final String relationPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
|
||||
|
||||
final String openorgsMergeRelsPath = DedupUtility
|
||||
.createOpenorgsMergeRelsPath(workingPath, actionSetId, subEntity);
|
||||
|
||||
final int maxIterations = dedupConf.getWf().getMaxIterations();
|
||||
log.info("Max iterations {}", maxIterations);
|
||||
|
||||
|
|
@ -105,67 +110,103 @@ public class SparkRemoveDiffRels extends AbstractSparkAction {
|
|||
.where("relClass == 'merges'")
|
||||
.toJavaRDD();
|
||||
|
||||
System.out.println("mergeRelsRDD = " + mergeRelsRDD.count());
|
||||
|
||||
// JavaRDD<Tuple2<Tuple2<String, String>, String>> diffRelsRDD = spark
|
||||
// .read()
|
||||
// .textFile(relationPath)
|
||||
// .map(patchRelFn(), Encoders.bean(Relation.class))
|
||||
// .toJavaRDD()
|
||||
// .filter(r -> filterRels(r, entity))
|
||||
// .map(rel -> {
|
||||
// if (rel.getSource().compareTo(rel.getTarget()) < 0)
|
||||
// return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "diffRel");
|
||||
// else
|
||||
// return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "diffRel");
|
||||
// });
|
||||
// THIS IS FOR TESTING PURPOSE
|
||||
JavaRDD<Tuple2<Tuple2<String, String>, String>> diffRelsRDD = spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(patchRelFn(), Encoders.bean(Relation.class))
|
||||
.load(mergeRelsPath)
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(r -> filterRels(r, entity))
|
||||
.map(rel -> {
|
||||
if (rel.getSource().compareTo(rel.getTarget()) < 0)
|
||||
return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "diffRel");
|
||||
else
|
||||
return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "diffRel");
|
||||
})
|
||||
.distinct();
|
||||
|
||||
System.out.println("diffRelsRDD = " + diffRelsRDD.count());
|
||||
|
||||
// JavaRDD<Tuple2<Tuple2<String, String>, String>> flatMergeRels = mergeRelsRDD
|
||||
// .mapToPair(rel -> new Tuple2<>(rel.getSource(), rel.getTarget()))
|
||||
// .groupByKey()
|
||||
// .flatMap(g -> {
|
||||
// List<Tuple2<Tuple2<String, String>, String>> rels = new ArrayList<>();
|
||||
//
|
||||
// List<String> ids = StreamSupport
|
||||
// .stream(g._2().spliterator(), false)
|
||||
// .collect(Collectors.toList());
|
||||
//
|
||||
// for (int i = 0; i < ids.size(); i++) {
|
||||
// for (int j = i + 1; j < ids.size(); j++) {
|
||||
// if (ids.get(i).compareTo(ids.get(j)) < 0)
|
||||
// rels.add(new Tuple2<>(new Tuple2<>(ids.get(i), ids.get(j)), g._1()));
|
||||
// else
|
||||
// rels.add(new Tuple2<>(new Tuple2<>(ids.get(j), ids.get(i)), g._1()));
|
||||
// }
|
||||
// }
|
||||
// return rels.iterator();
|
||||
//
|
||||
// });
|
||||
JavaRDD<Tuple2<Tuple2<String, String>, String>> mergeRels = mergeRelsRDD
|
||||
.map(rel -> {
|
||||
if (rel.getSource().compareTo(rel.getTarget()) < 0)
|
||||
return new Tuple2<>(new Tuple2<>(rel.getSource(), rel.getTarget()), "mergeRel");
|
||||
else
|
||||
return new Tuple2<>(new Tuple2<>(rel.getTarget(), rel.getSource()), "mergeRel");
|
||||
});
|
||||
System.out.println("mergeRelsProcessed = " + mergeRels.count());
|
||||
|
||||
JavaRDD<Tuple2<Tuple2<String, String>, String>> flatMergeRels = mergeRelsRDD
|
||||
.mapToPair(rel -> new Tuple2<>(rel.getSource(), rel.getTarget()))
|
||||
.groupByKey()
|
||||
.flatMap(g -> {
|
||||
List<Tuple2<Tuple2<String, String>, String>> rels = new ArrayList<>();
|
||||
|
||||
List<String> ids = StreamSupport
|
||||
.stream(g._2().spliterator(), false)
|
||||
.collect(Collectors.toList());
|
||||
|
||||
for (int i = 0; i < ids.size(); i++) {
|
||||
for (int j = i + 1; j < ids.size(); j++) {
|
||||
if (ids.get(i).compareTo(ids.get(j)) < 0)
|
||||
rels.add(new Tuple2<>(new Tuple2<>(ids.get(i), ids.get(j)), g._1()));
|
||||
else
|
||||
rels.add(new Tuple2<>(new Tuple2<>(ids.get(j), ids.get(i)), g._1()));
|
||||
}
|
||||
}
|
||||
return rels.iterator();
|
||||
|
||||
});
|
||||
|
||||
JavaRDD<Relation> purgedMergeRels = flatMergeRels
|
||||
// JavaRDD<Relation> purgedMergeRels = flatMergeRels
|
||||
// .union(diffRelsRDD)
|
||||
// .mapToPair(rel -> new Tuple2<>(rel._1(), Arrays.asList(rel._2())))
|
||||
// .reduceByKey((a, b) -> {
|
||||
// List<String> list = new ArrayList<String>();
|
||||
// list.addAll(a);
|
||||
// list.addAll(b);
|
||||
// return list;
|
||||
// })
|
||||
// .filter(rel -> rel._2().size() == 1)
|
||||
// .mapToPair(rel -> new Tuple2<>(rel._2().get(0), rel._1()))
|
||||
// .flatMap(rel -> {
|
||||
// List<Tuple2<String, String>> rels = new ArrayList<>();
|
||||
// String source = rel._1();
|
||||
// rels.add(new Tuple2<>(source, rel._2()._1()));
|
||||
// rels.add(new Tuple2<>(source, rel._2()._2()));
|
||||
// return rels.iterator();
|
||||
// })
|
||||
// .distinct()
|
||||
// .flatMap(rel -> tupleToMergeRel(rel, dedupConf));
|
||||
JavaRDD<Relation> purgedMergeRels = mergeRels
|
||||
.union(diffRelsRDD)
|
||||
.mapToPair(rel -> new Tuple2<>(rel._1(), Arrays.asList(rel._2())))
|
||||
.reduceByKey((a, b) -> {
|
||||
List<String> list = new ArrayList<String>();
|
||||
list.addAll(a);
|
||||
list.addAll(b);
|
||||
return list;
|
||||
})
|
||||
.filter(rel -> rel._2().size() == 1)
|
||||
.mapToPair(rel -> new Tuple2<>(rel._2().get(0), rel._1()))
|
||||
.flatMap(rel -> {
|
||||
List<Tuple2<String, String>> rels = new ArrayList<>();
|
||||
String source = rel._1();
|
||||
rels.add(new Tuple2<>(source, rel._2()._1()));
|
||||
rels.add(new Tuple2<>(source, rel._2()._2()));
|
||||
return rels.iterator();
|
||||
})
|
||||
.distinct()
|
||||
.flatMap(rel -> tupleToMergeRel(rel, dedupConf));
|
||||
.mapToPair(t -> new Tuple2<>(t._1()._1() + "|||" + t._1()._2(), t._2()))
|
||||
.groupByKey()
|
||||
.filter(g -> Iterables.size(g._2()) == 1)
|
||||
.flatMap(
|
||||
t -> tupleToMergeRel(
|
||||
new Tuple2<>(t._1().split("\\|\\|\\|")[0], t._1().split("\\|\\|\\|")[1]),
|
||||
dedupConf));
|
||||
|
||||
System.out.println("purgedMergeRels = " + purgedMergeRels.count());
|
||||
|
||||
spark
|
||||
.createDataset(purgedMergeRels.rdd(), Encoders.bean(Relation.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.json(mergeRelsPath);
|
||||
.json(openorgsMergeRelsPath);
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,108 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class OrgSimRel implements Serializable {
|
||||
|
||||
String local_id;
|
||||
String oa_original_id;
|
||||
String oa_name;
|
||||
String oa_acronym;
|
||||
String oa_country;
|
||||
String oa_url;
|
||||
String oa_collectedfrom;
|
||||
String group_id;
|
||||
|
||||
public OrgSimRel() {
|
||||
}
|
||||
|
||||
public OrgSimRel(String local_id, String oa_original_id, String oa_name, String oa_acronym, String oa_country,
|
||||
String oa_url, String oa_collectedfrom, String group_id) {
|
||||
this.local_id = local_id;
|
||||
this.oa_original_id = oa_original_id;
|
||||
this.oa_name = oa_name;
|
||||
this.oa_acronym = oa_acronym;
|
||||
this.oa_country = oa_country;
|
||||
this.oa_url = oa_url;
|
||||
this.oa_collectedfrom = oa_collectedfrom;
|
||||
this.group_id = group_id;
|
||||
}
|
||||
|
||||
public String getLocal_id() {
|
||||
return local_id;
|
||||
}
|
||||
|
||||
public void setLocal_id(String local_id) {
|
||||
this.local_id = local_id;
|
||||
}
|
||||
|
||||
public String getOa_original_id() {
|
||||
return oa_original_id;
|
||||
}
|
||||
|
||||
public void setOa_original_id(String oa_original_id) {
|
||||
this.oa_original_id = oa_original_id;
|
||||
}
|
||||
|
||||
public String getOa_name() {
|
||||
return oa_name;
|
||||
}
|
||||
|
||||
public void setOa_name(String oa_name) {
|
||||
this.oa_name = oa_name;
|
||||
}
|
||||
|
||||
public String getOa_acronym() {
|
||||
return oa_acronym;
|
||||
}
|
||||
|
||||
public void setOa_acronym(String oa_acronym) {
|
||||
this.oa_acronym = oa_acronym;
|
||||
}
|
||||
|
||||
public String getOa_country() {
|
||||
return oa_country;
|
||||
}
|
||||
|
||||
public void setOa_country(String oa_country) {
|
||||
this.oa_country = oa_country;
|
||||
}
|
||||
|
||||
public String getOa_url() {
|
||||
return oa_url;
|
||||
}
|
||||
|
||||
public void setOa_url(String oa_url) {
|
||||
this.oa_url = oa_url;
|
||||
}
|
||||
|
||||
public String getOa_collectedfrom() {
|
||||
return oa_collectedfrom;
|
||||
}
|
||||
|
||||
public void setOa_collectedfrom(String oa_collectedfrom) {
|
||||
this.oa_collectedfrom = oa_collectedfrom;
|
||||
}
|
||||
|
||||
public String getGroup_id() {
|
||||
return group_id;
|
||||
}
|
||||
|
||||
public void setGroup_id(String group_id) {
|
||||
this.group_id = group_id;
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return "OrgSimRel{" +
|
||||
"local_id='" + local_id + '\'' +
|
||||
", oa_original_id='" + oa_original_id + '\'' +
|
||||
", oa_name='" + oa_name + '\'' +
|
||||
", oa_acronym='" + oa_acronym + '\'' +
|
||||
", oa_country='" + oa_country + '\'' +
|
||||
", oa_url='" + oa_url + '\'' +
|
||||
", oa_collectedfrom='" + oa_collectedfrom + '\'' +
|
||||
'}';
|
||||
}
|
||||
}
|
||||
|
|
@ -79,7 +79,7 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resetWorkingPath"/>
|
||||
<start to="resetOrgSimRels"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
|
|
@ -88,8 +88,9 @@
|
|||
<action name="resetOrgSimRels">
|
||||
<fs>
|
||||
<delete path="${workingPath}/${actionSetId}/organization_simrel"/>
|
||||
<delete path="${workingPath}/${actionSetId}/organization_mergerel"/>
|
||||
</fs>
|
||||
<ok to="copySimRels"/>
|
||||
<ok to="CreateSimRels"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
|
@ -120,7 +121,7 @@
|
|||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- copy similarity relations coming from openorgs in order to improve dedup quality -->
|
||||
<!-- copy simrels relations coming from openorgs -->
|
||||
<action name="CopyOpenorgsSimRels">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
|
@ -139,6 +140,7 @@
|
|||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--numPartitions</arg><arg>8000</arg>
|
||||
|
|
@ -170,33 +172,6 @@
|
|||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
|
||||
</spark>
|
||||
<ok to="RemoveDifferences"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="RemoveDifferences">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Create Merge Relations</name>
|
||||
<class>eu.dnetlib.dhp.oa.dedup.SparkRemoveDiffRels</class>
|
||||
<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
|
||||
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||
<arg>--actionSetId</arg><arg>${actionSetId}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--numPartitions</arg><arg>8000</arg>
|
||||
</spark>
|
||||
<ok to="PrepareOrgRels"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,62 @@
|
|||
[
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "graphBasePath",
|
||||
"paramDescription": "the base path of raw graph",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "w",
|
||||
"paramLongName": "workingPath",
|
||||
"paramDescription": "the working directory path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "la",
|
||||
"paramLongName": "isLookUpUrl",
|
||||
"paramDescription": "the url of the lookup service",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "asi",
|
||||
"paramLongName": "actionSetId",
|
||||
"paramDescription": "the id of the actionset (orchestrator)",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "nc",
|
||||
"paramLongName": "numConnections",
|
||||
"paramDescription": "number of connections to the postgres db (for the write operation)",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "au",
|
||||
"paramLongName": "apiUrl",
|
||||
"paramDescription": "the url for the APIs of the openorgs service",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "du",
|
||||
"paramLongName": "dbUrl",
|
||||
"paramDescription": "the url of the database",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "dusr",
|
||||
"paramLongName": "dbUser",
|
||||
"paramDescription": "the user of the database",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "t",
|
||||
"paramLongName": "dbTable",
|
||||
"paramDescription": "the name of the table in the database",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "dpwd",
|
||||
"paramLongName": "dbPwd",
|
||||
"paramDescription": "the password for the user of the database",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,56 @@
|
|||
[
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "graphBasePath",
|
||||
"paramDescription": "the base path of raw graph",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "w",
|
||||
"paramLongName": "workingPath",
|
||||
"paramDescription": "the working directory path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "la",
|
||||
"paramLongName": "isLookUpUrl",
|
||||
"paramDescription": "the url of the lookup service",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "asi",
|
||||
"paramLongName": "actionSetId",
|
||||
"paramDescription": "the id of the actionset (orchestrator)",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "nc",
|
||||
"paramLongName": "numConnections",
|
||||
"paramDescription": "number of connections to the postgres db (for the write operation)",
|
||||
"paramRequired": false
|
||||
},
|
||||
{
|
||||
"paramName": "du",
|
||||
"paramLongName": "dbUrl",
|
||||
"paramDescription": "the url of the database",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "dusr",
|
||||
"paramLongName": "dbUser",
|
||||
"paramDescription": "the user of the database",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "t",
|
||||
"paramLongName": "dbTable",
|
||||
"paramDescription": "the name of the table in the database",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "dpwd",
|
||||
"paramLongName": "dbPwd",
|
||||
"paramDescription": "the password for the user of the database",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -0,0 +1,296 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
|
||||
import static org.apache.spark.sql.functions.count;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.IOException;
|
||||
import java.io.Serializable;
|
||||
import java.net.URISyntaxException;
|
||||
import java.nio.file.Paths;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.Mockito;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import jdk.nashorn.internal.ir.annotations.Ignore;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
public class SparkOpenorgsTest implements Serializable {
|
||||
|
||||
@Mock(serializable = true)
|
||||
ISLookUpService isLookUpService;
|
||||
|
||||
private static SparkSession spark;
|
||||
private static JavaSparkContext jsc;
|
||||
|
||||
private static String testGraphBasePath;
|
||||
private static String testOutputBasePath;
|
||||
private static String testDedupGraphBasePath;
|
||||
private static final String testActionSetId = "test-orchestrator";
|
||||
|
||||
protected static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
@BeforeAll
|
||||
public static void cleanUp() throws IOException, URISyntaxException {
|
||||
|
||||
testGraphBasePath = Paths
|
||||
.get(SparkOpenorgsTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
|
||||
.toFile()
|
||||
.getAbsolutePath();
|
||||
testOutputBasePath = createTempDirectory(SparkOpenorgsTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
testDedupGraphBasePath = createTempDirectory(SparkOpenorgsTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
||||
// FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
FileUtils.deleteDirectory(new File("/tmp/test-orchestrator/organization_openorgs_mergerels"));
|
||||
|
||||
final SparkConf conf = new SparkConf();
|
||||
conf.set("spark.sql.shuffle.partitions", "200");
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(SparkDedupTest.class.getSimpleName())
|
||||
.master("local[*]")
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
|
||||
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
public void setUp() throws IOException, ISLookUpException {
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains(testActionSetId)))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator_openorgs.xml")));
|
||||
|
||||
lenient()
|
||||
.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
|
||||
.thenReturn(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkDedupTest.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void copyOpenorgsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyOpenorgs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/copyOpenorgs_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-w", testOutputBasePath,
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCopyOpenorgs(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_deduprecord = jsc
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
|
||||
.count();
|
||||
|
||||
assertEquals(0, orgs_deduprecord);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void copyOpenorgsMergeRels() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyOpenorgsMergeRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-w", testOutputBasePath,
|
||||
"-la", "lookupurl",
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCopyOpenorgsMergeRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_mergerel = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
|
||||
assertEquals(0, orgs_mergerel);
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void copyOpenorgsSimRels() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyOpenorgsSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/copyOpenorgsMergeRels_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-w", testOutputBasePath,
|
||||
"-la", "lookupurl",
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCopyOpenorgsSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel = spark
|
||||
.read()
|
||||
.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
|
||||
.count();
|
||||
|
||||
System.out.println("orgs_simrel = " + orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void createSimRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-asi", testActionSetId,
|
||||
"-la", "lookupurl",
|
||||
"-w", "/tmp",
|
||||
"-np", "50"
|
||||
});
|
||||
|
||||
new SparkCreateSimRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_simrel = spark
|
||||
.read()
|
||||
.textFile("/tmp/" + testActionSetId + "/organization_simrel")
|
||||
.count();
|
||||
|
||||
assertEquals(3082, orgs_simrel);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void createMergeRelsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateMergeRels.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i",
|
||||
testGraphBasePath,
|
||||
"-asi",
|
||||
testActionSetId,
|
||||
"-la",
|
||||
"lookupurl",
|
||||
"-w",
|
||||
"/tmp"
|
||||
});
|
||||
|
||||
new SparkCreateMergeRels(parser, spark).run(isLookUpService);
|
||||
|
||||
long orgs_mergerel = spark
|
||||
.read()
|
||||
.load("/tmp/" + testActionSetId + "/organization_mergerel")
|
||||
.count();
|
||||
assertEquals(1272, orgs_mergerel);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void copyRelationsNoOpenorgsTest() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyRelationsNoOpenorgs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath,
|
||||
"-w", testOutputBasePath,
|
||||
"-o", testDedupGraphBasePath
|
||||
});
|
||||
|
||||
new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
|
||||
|
||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||
|
||||
// Dataset<Relation> relsRDD = spark.read().textFile(testDedupGraphBasePath + "/relation").map(patchRelFn(), Encoders.bean(Relation.class));
|
||||
|
||||
assertEquals(500, relations);
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void finalCleanUp() throws IOException {
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
}
|
||||
|
||||
private static MapFunction<String, Relation> patchRelFn() {
|
||||
return value -> {
|
||||
final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);
|
||||
if (rel.getDataInfo() == null) {
|
||||
rel.setDataInfo(new DataInfo());
|
||||
}
|
||||
return rel;
|
||||
};
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,24 @@
|
|||
<RESOURCE_PROFILE>
|
||||
<HEADER>
|
||||
<RESOURCE_IDENTIFIER value=""/>
|
||||
<RESOURCE_TYPE value="DedupOrchestrationDSResourceType"/>
|
||||
<RESOURCE_KIND value="DedupOrchestrationDSResources"/>
|
||||
<RESOURCE_URI value=""/>
|
||||
<DATE_OF_CREATION value="2001-12-31T12:00:00"/>
|
||||
</HEADER>
|
||||
<BODY>
|
||||
<CONFIGURATION enabled="true">
|
||||
<DEDUPLICATION>
|
||||
<ENTITY code="20" label="Organization" name="organization"/>
|
||||
<ACTION_SET id="test-orchestrator"/>
|
||||
<SCAN_SEQUENCE>
|
||||
<SCAN id="organization"/>
|
||||
</SCAN_SEQUENCE>
|
||||
</DEDUPLICATION>
|
||||
</CONFIGURATION>
|
||||
<STATUS>
|
||||
<LAST_UPDATE value="2001-12-31T12:00:00"/>
|
||||
</STATUS>
|
||||
<SECURITY_PARAMETERS>SECURITY_PARAMETERS</SECURITY_PARAMETERS>
|
||||
</BODY>
|
||||
</RESOURCE_PROFILE>
|
||||
|
|
@ -612,7 +612,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
|
|||
final DataInfo info = prepareDataInfo(rs); // TODO
|
||||
|
||||
final String orgId1 = createOpenaireId(20, rs.getString("id1"), true);
|
||||
final String orgId2 = createOpenaireId(40, rs.getString("id2"), true);
|
||||
final String orgId2 = createOpenaireId(20, rs.getString("id2"), true);
|
||||
final String relClass = rs.getString("relclass");
|
||||
|
||||
final List<KeyValue> collectedFrom = listKeyValues(
|
||||
|
|
|
|||
Loading…
Reference in New Issue